hDbr1 is a nucleocytoplasmic shuttling protein with a protein phosphatase-like motif essential for debranching activity

Kataoka, Naoyuki; Dobashi, Izumi; Hagiwara, Masatoshi; Ohno, Masatomi

doi:10.1038/srep01090

Cited by 16 publications

(30 citation statements)

References 51 publications

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“…Transient expression of DBR1-RFP in tobacco as well as transgenic Arabidopsis plants expressing DBR1-GFP showed that DBR1 was distributed in both the nucleus and cytoplasm (Fig 6A), which is consistent with the finding that DBR1 is a nucleocytoplasmic shuttling protein in humans [37]. The DBR1-2 mutant protein did not affect the distribution of DBR1 (S6A Fig).…”

Section: Resultssupporting

confidence: 87%

Intron Lariat RNA Inhibits MicroRNA Biogenesis by Sequestering the Dicing Complex in Arabidopsis

Wang

Junfeng

et al. 2016

PLoS Genet

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Lariat RNAs formed as by-products of splicing are quickly degraded by the RNA debranching enzyme 1 (DBR1), leading to their turnover. Null dbr1 mutants in both animals and plants are embryo lethal, but the mechanism underlying the lethality remains unclear. Here we characterized a weak mutant allele of DBR1 in Arabidopsis, dbr1-2, and showed that a global increase in lariat RNAs was unexpectedly accompanied by a genome-wide reduction in miRNA accumulation. The dbr1-2 mutation had no effects on expression of miRNA biogenesis genes or primary miRNAs (pri-miRNAs), but the association of pri-miRNAs with the DCL1/HYL1 dicing complex was impaired. Lariat RNAs were associated with the DCL1/HYL1 dicing complex in vivo and competitively inhibited the binding of HYL1 with pri-miRNA. Consistent with the impacts of lariat RNAs on miRNA biogenesis, over-expression of lariat RNAs reduced miRNA accumulation. Lariat RNAs localized in nuclear bodies, and partially co-localize with HYL1, and both DCL1 and HYL1 were mis-localized in dbr1-2. Together with our findings that nearly four hundred lariat RNAs exist in wild type plants and that these lariat RNAs also associate with the DCL1/HYL1 dicing complex in vivo, we thus propose that lariat RNAs, as decoys, inhibit miRNA processing, suggesting a hitherto unknown layer of regulation in miRNA biogenesis.

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Section: Resultssupporting

confidence: 87%

Intron Lariat RNA Inhibits MicroRNA Biogenesis by Sequestering the Dicing Complex in Arabidopsis

Wang

Junfeng

et al. 2016

PLoS Genet

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“…Debranching of these lariat-intermediates by Dbr1 comprises a quality control mechanism for lariat-intermediates that do not complete splicing and escape into the cytoplasm (Hilleren and Parker 2003). Shuttling of human Dbr1 between the nucleus and cytoplasm is dynamic (Kataoka et al 2013), and phosphorylated forms of both Dbr1 and Drn1 have been detected by proteomic analysis (Stark et al 2010), suggesting that RNA turnover by debranching is subject to regulation by both localization and post-translational modification. We characterized a novel splicing factor, Drn1/Ygr093w, in Saccharomyces cerevisiae that modulates the turnover of branched RNAs by Dbr1.…”

Section: Introductionmentioning

confidence: 99%

A homolog of lariat-debranching enzyme modulates turnover of branched RNA

Garrey

Katolik

Prekeris

et al. 2014

RNA

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Turnover of the branched RNA intermediates and products of pre-mRNA splicing is mediated by the lariat-debranching enzyme Dbr1. We characterized a homolog of Dbr1 from Saccharomyces cerevisiae, Drn1/Ygr093w, that has a pseudometallophosphodiesterase domain with primary sequence homology to Dbr1 but lacks essential active site residues found in Dbr1. Whereas loss of Dbr1 results in lariat-introns failing broadly to turnover, loss of Drn1 causes low levels of lariat-intron accumulation. Conserved residues in the Drn1 C-terminal CwfJ domains, which are not present in Dbr1, are required for efficient intron turnover. Drn1 interacts with Dbr1, components of the Nineteen Complex, U2 snRNA, branched intermediates, and products of splicing. Drn1 enhances debranching catalyzed by Dbr1 in vitro, but does so without significantly improving the affinity of Dbr1 for branched RNA. Splicing carried out in in vitro extracts in the absence of Drn1 results in an accumulation of branched splicing intermediates and products released from the spliceosome, likely due to less active debranching, as well as the promiscuous release of cleaved 5 ′ -exon. Drn1 enhances Dbr1-mediated turnover of lariat-intermediates and lariat-intron products, indicating that branched RNA turnover is regulated at multiple steps during splicing.

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“…It is highly likely that rapid and correct intron turnover processes including RNA lariat debranching reaction is critical for higher eukaryotes. In addition to a catalytic GNHE motif, human Dbr1 (hDbr1) protein has a bipartite type nuclear localization signal (NLS) ( Figure 1A) and it is a nucleo-cytoplasmic protein ( Figure 1B), while the steady state subcellular localization of hDbr1 is in the nucleoplasm [13] . This finding strongly suggests that hDbr1 has role(s) in both in the nucleus and in the cytoplasm.…”

Section: Research Highlightmentioning

confidence: 99%

“…well conserved among many species and this protein shares a protein phosphatase catalytic motif, GNHE motif, as a catalytic center ( Figure 1A) [13,14] . Dbr1 gene is not essential in Saccharomyces cerevisiae for cell viability, although Dbr1 mutant exhibits accumulation of lariat RNAs [17] .…”

Section: Research Highlightmentioning

confidence: 99%

“…Before lariat introns are degraded, a 2'-5' phosphodiester bond between branch point residue and the guanosine which resides at the end of the 5' splice site has to be dissolved. This reaction is called as debranching reaction, and it is mediated by an RNA lariat debranching enzyme, Debranching enzyme protein 1 (Dbr1) ( Figure 1A) [13][14][15][16][17][18] . Amino acid sequence of Dbr1 protein is…”

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confidence: 99%

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Human RNA lariat Debranching Enzyme Protein 1 –A surveillant for branch RNAs for degradation

Kataoka

2015

RNA Dis

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Splicing is a process to remove introns from precursor of mRNAs (pre-mRNAs). Introns are excised as a lariat form, and they should be debranched before degradation. Debranching reaction is conferred by a RNA lariat debranching enzyme 1 (Dbr1) protein. The Dbr1 protein is evolutionarily conserved among many species and shares GNHE motif for debranching activity that is identical to protein phosphatase activity center. The human Dbr1 protein has a bipartite type nuclear localization signal, and it shuttles between the nucleus and the cytoplasm, which suggests novel function(s) in the cytoplasm. The human Dbr1 protein interacts with two proteins, Xab2 and hDrn1. Since Xab2 is involved in both splicing and transcription-coupled DNA repair (TCR), hDbr1 may also have a role in TCR. Although the function of hDrn1 is not known yet, this protein specifically interact with carboxy terminal of hDbr1 and it is also a nucleo-cytoplasmic shuttling protein. A heterodimer of hDbr1-hDrn1 may have role(s) not only in the nucleus but also in the cytoplasm of human cells.Keywords: Splicing; debranching; Dbr1; lariat intron; nucleo-cytoplasmic shuttling To cite this article: Naoyuki Kataoka. Human RNA lariat debranching enzyme protein 1 -A surveillant for branch RNAs for degradation. RNA Dis 2015; 2: e963. doi: 10.14800/rd.963.In higher eukaryotes, most of nuclear-encoded genes are separated by introns [1] . Pre-mRNA splicing is to remove introns and connect exons, which is an essential step for gene expression. Introns are removed as a lariat form by a huge RNA-protein complex, spliceosome [2][3][4][5] . Excised introns are supposed to be restricted and get degraded in the nucleus. Although intron degradation pathway has not been well understood compared with the splicing reaction, this step is supposed to be very important especially in higher eukaryotes. For example, some of small nucleolar RNAs (snoRNAs) and microRNAs (miRNAs) are embedded in introns and the biogenesis of these noncoding RNAs is functionally associated with splicing reactions [6][7][8][9][10][11][12] . Splicing takes place in two catalytic steps [2][3][4][5] . As the first step, the 5' splice site is cleaved and the 5' end of the intron is linked to the branch point nucleotide by forming a 2'-5' phosphodiester bond ( Figure 1A). This produces splicing intermediates, such as 5' exon and a lariat form intron RNA with 3' exon. Then they undergo the second step reaction that the cleavage at 3' splice site takes place and two exons are concurrently ligated to generate mRNA ( Figure 1B). Upon the completion of the second step reaction, the spliceosome is dismantled into two RNA-protein complexes, spliced mRNA-protein complex and lariat-intron containing RNA-protein complex. The lariat-intron complex undergoes intron degradation processes. Before lariat introns are degraded, a 2'-5' phosphodiester bond between branch point residue and the guanosine which resides at the end of the 5' splice site has to be dissolved. This reaction is called as debranching reaction, and i...

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hDbr1 is a nucleocytoplasmic shuttling protein with a protein phosphatase-like motif essential for debranching activity

Cited by 16 publications

References 51 publications

Intron Lariat RNA Inhibits MicroRNA Biogenesis by Sequestering the Dicing Complex in Arabidopsis

Intron Lariat RNA Inhibits MicroRNA Biogenesis by Sequestering the Dicing Complex in Arabidopsis

A homolog of lariat-debranching enzyme modulates turnover of branched RNA

Human RNA lariat Debranching Enzyme Protein 1 –A surveillant for branch RNAs for degradation

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